, Nicolas Brich, Michael Krone, Martin Nöllenburg, Jiacheng Yu, Hiroaki Natsukawa, Xiaoru Yuan, Hsiang-Yun WuAn introduction to and survey of biological network visualization
COMPUTERS & GRAPHICS-UK, 126, February 2025.
Henry Ehlers, Nicolas Brich, Michael Krone, Martin Nöllenburg, Jiacheng Yu, Hiroaki Natsukawa, Xiaoru Yuan, Hsiang-Yun Wu
An introduction to and survey of biological network visualization
COMPUTERS & GRAPHICS-UK, 126, February 2025.
Johannes Eschner, Peter Mindek, Manuela Waldner
Illustrative Motion Smoothing for Attention Guidance in Dynamic Visualizations
Computer Graphics Forum, 42(3):361-372, June 2023. [
paper] [
video]
Johannes Eschner
Generating Molecular Motion Blur Videos for a User Study
[
project report]
Pavol Ulbrich, Manuela Waldner, Katarína Furmanová, Sergio M. Margues, David Bednář, Barbora Kozlikova, Jan Byska
sMolBoxes: Dataflow Model for Molecular Dynamics Exploration
IEEE Transactions on Visualization and Computer Graphics:1-10, October 2022. [arxiv]
Ruwayda Alharbi, Ondrej Strnad, Laura R. Luidolt, Manuela Waldner, David Kouřil, Ciril Bohak, Tobias Klein, Eduard Gröller, Ivan Viola
Nanotilus: Generator of Immersive Guided-Tours in Crowded 3D Environments
IEEE Transactions on Visualization and Computer Graphics:1-16, December 2021. [
Image] [
Paper]
David Kouřil, Ondrej Strnad, Peter Mindek, Sarkis Halladjian, Tobias Isenberg, Eduard Gröller, Ivan Viola
Molecumentary: Adaptable Narrated Documentaries Using Molecular Visualization
IEEE Transactions on Visualization and Computer Graphics, 1:1-1, November 2021.
David Kouřil
Interactive Visualization of Dense and Multi-Scale Data for Science Outreach
Supervisor: Ivan Viola
Duration: March 2017 — April 2021
[
teaser] [
thesis]
Sarkis Halladjian, David Kouřil, Haichao Miao, Eduard Gröller, Ivan Viola, Tobias Isenberg
Multiscale Unfolding: Illustratively Visualizing the Whole Genome at a Glance
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS , 3:1-13, March 2021. [
Image] [
Paper]
Henry Ehlers
Unknown
Supervisor: Renata Raidou
Duration: 2021 — 2024
Hsiang-Yun Wu, Martin Nöllenburg, Ivan Viola
Multi-level Area Balancing of Clustered Graphs
IEEE Transactions on Visualization and Computer Graphics (TVCG), x:1-15, November 2020. [
paper] [
video]
Ladislav Čmolík, Václav Pavlovec, Hsiang-Yun Wu, Martin Nöllenburg
Mixed Labeling: Integrating Internal and External Labels
IEEE Transactions on Visualization and Computer Graphics (TVCG), x:1-14, September 2020. [
image] [
paper]
Milena Nowak
Hierarchical Multi-resolution Data Structure for Molecular Visualization
[
Image] [
Master Thesis]
Elisa De Llano, Haichao Miao, Yasaman Ahmadi, Armanda J Wilson, Morgan Beeby, Ivan Viola, Ivan Barisic
Adenita: interactive 3D modelling and visualization of DNA nanostructures
Nucleic Acids Research, July 2020.
Renata Raidou, Barbora Kozlikova, Johanna Beyer, Timo Ropinski, Issei Fujishiro
NII Shonan Meeting Report No. 167: Formalizing Biological and Medical Visualization
ISSN 2186-7437
Sarkis Halladjian, Haichao Miao, David Kouřil, Eduard Gröller, Ivan Viola, Tobias Isenberg
ScaleTrotter: Illustrative Visual Travels Across Negative Scales
IEEE Transactions on Visualization and Computer Graphics, 26(1), January 2020. [
paper]
Ngan Nguyen, Ondrej Strnad, Tobias Klein, Ruwayda Alharbi, Peter Wonka, Martina Maritan, Peter Mindek, Ludovic Autin, David Goodsell, Ivan Viola
Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models
IEEE Transactions on Visualization and Computer Graphics, 2020.
Tobias Klein
Instant Construction of Atomistic Models for Visualization in Integrative Cell Biology
Supervisor: Ivan Viola
Duration: 2016 — 2019
[
image]
Tobias Klein, Peter Mindek, Ludovic Autin, David Goodsell, Arthur Olson, Eduard Gröller, Ivan Viola
Parallel Generation and Visualization of Bacterial Genome Structures
Computer Graphics Forum, 38(7):57-68, November 2019.
Hsiang-Yun Wu, Martin Nöllenburg, Ivan Viola
Graph Models for Biological Pathway Visualization: State of the Art and Future Challenges,
20. October 2019, Vis 2019 Workshop, Canada
[
paper]
Susanne Rinortner
Visualizing Protein Interactions in Corresponding Compartments
Aleksandr Amirkhanov, Ilona Kosiuk, Peter Szmolyan, Artem Amirkhanov, Gabriel Mistelbauer, Eduard Gröller, Renata Raidou
ManyLands: A Journey Across 4D Phase Space of Trajectories
Computer Graphics Forum, 38(7):191-202, October 2019. [
Paper] [
Video demo]
Hsiang-Yun Wu, Martin Nöllenburg, Ivan Viola
Map of Metabolic Harmony
[
image-full]
Maximilian Sbardellati, Haichao Miao, Hsiang-Yun Wu, Eduard Gröller, Ivan Barisic, Ivan Viola
Interactive Exploded Views for Molecular Structures
In Proceedings of the 9th Eurographics Workshop on Visual Computing for Biology and Medicine, pages 103-112. September 2019.
[
paper]
Haichao Miao
Geometric Abstraction for Effective Visualization and Modeling
Supervisor: Ivan Viola
Tobias Klein, Ivan Viola, Eduard Gröller, Peter Mindek
Multi-Scale Procedural Animations of Microtubule Dynamics Based on Measured Data
IEEE Transactions on Visualization and Computer Graphics, 26(1):622-632, August 2019. [
paper]
Renata Raidou
Visual Analytics for the Representation, Exploration and Analysis of High-Dimensional, Multi-Faceted Medical Data
In Biomedical Visualisation, pages 137-162, July 2019
Jan Byska, Thomas Trautner, Sergio Marques, Jiri Damborsky, Barbora Kozlikova, Manuela Waldner
Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization
Computer Graphics Forum, 38(3):441-453, June 2019. [
paper] [
video]
Haichao Miao, Elisa De Llano, Ivan Viola, Ivan Barisic
Interactive Visual Analysis for the Design of DNA Nanostructures
Poster shown at NANTECH 2019 – Nucleic Acid Nanotechnology: From Algorithmic Design to Biochemical Applications – Espoo, Finland
(27. May 2019-29. May 2019)
Hsiang-Yun Wu, Martin Nöllenburg, Filipa L. Sousa, Ivan Viola
Metabopolis: Scalable Network Layout for Biological Pathway Diagrams in Urban Map Style
BMC Bioinformatics, 20(187):1-20, May 2019. [
paper] [video]
Hsiang-Yun Wu, Haichao Miao, Ivan Viola
From Cells to Atoms - Biological Information Visualization (in Chinese)
TR-193-02-2019-1, March 2019 [
paper]
Nicholas Waldin, Manuela Waldner, Mathieu Le Muzic, Eduard Gröller, David Goodsell, Ludovic Autin, Arthur Olson, Ivan Viola
Cuttlefish: Color Mapping for Dynamic Multi‐Scale Visualizations
Computer Graphics Forum, 38(6):150-164, March 2019. [Open Access Article in Wiley Online Library]
Felix Kugler
Profiling and Optimization of Large Biomolecular Scenes
[
image] [
thesis]
Katharina Unger
Visual Comparison of Organism-Specific Metabolic Pathways
[
CESCG paper]
Johannes Weissenböck, Bernhard Fröhler, Eduard Gröller, Johann Kastner, Christoph Heinzl
Dynamic Volume Lines: Visual Comparison of 3D Volumes through Space-filling Curves
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 25(1):1040-1049, January 2019. [
image]
Haichao Miao, Tobias Klein, David Kouřil, Peter Mindek, Karsten Schatz, Eduard Gröller, Barbora Kozlikova, Tobias Isenberg, Ivan Viola
Multiscale Molecular Visualization
Journal of Molecular Biology, 6(31):1049-1070, January 2019. [
Paper]
Aleksandr Amirkhanov, Ilona Kosiuk, Peter Szmolyan, Artem Amirkhanov, Gabriel Mistelbauer, Eduard Gröller, Renata Raidou
EG VCBM 2019 Image Contest Award, people's choice—ManyLands: A Journey Across 4D Phase Space of Biological Systems
Peter Mindek
Molecular Visualization,
10. November 2018, FYI: Informationsdesign Konferenz Wien, Nordbahn-Halle, Vienna
Maximilian Sbardellati
Interactive Exploded Views for Presenting DNA Nano-Structures
[
image]
Thomas Trautner
Importance-Driven Exploration of Molecular Dynamics Simulations
[
image] [
Poster]
Nicolas Grossmann, Thomas Köppel, Eduard Gröller, Renata Raidou
VisualFlatter - Visual Analysis of Distortions in the Projection of Biomedical Structures
Eurographics Proceedings, September 2018.
Elisa De Llano, Haichao Miao, Tobias Isenberg, Eduard Gröller, Ivan Viola, Ivan Barisic
A Preview to Adenita: Visualization and Modeling of DNA Nanostructures
Poster shown at 3rd Functional DNA Nanotechnology Workshop
( 6. June 2018- 8. June 2018)
Haichao Miao, Elisa De Llano, Tobias Isenberg, Eduard Gröller, Ivan Barisic, Ivan Viola
DimSUM: Dimension and Scale Unifying Maps for Visual Abstraction of DNA Origami Structures
Computer Graphics Forum, 37(3), June 2018. [
Paper]
Hsiang-Yun Wu, Martin Nöllenburg, Ivan Viola
A Visual Comparison of Hand-Drawn and Machine-Generated Human Metabolic Pathways
Poster shown at EuroVis
( 4. June 2018- 8. June 2018)
[
poster]
Katarína Furmanová, Jan Byska, Eduard Gröller, Ivan Viola, Jan J. Paleček, Barbora Kozlikova
COZOID: contact zone identifier for visual analysis of protein-protein interactions
BMC Bioinformatics, (19:125 ):1-25, April 2018. [
image] [
Paper]
Hsiang-Yun Wu, Martin Nöllenburg, Ivan Viola
The Travel of a Metabolite
submitted to PacificVis 2018 Data Story Telling Contest
[
paper] [
video]
Thomas Bernhard Koch
Semantic Screen-Space Occlusion for Multiscale Molecular Visualization
[
Bachelor Thesis]
Julian Strohmayer
A Visual Analytics Approach to Hypocotyl/Root Transition Detection in Arabidopsis Thaliana
[
image]
Haichao Miao, Elisa De Llano, Johannes Sorger, Yasaman Ahmadi, Tadija Kekic, Tobias Isenberg, Eduard Gröller, Ivan Barisic, Ivan Viola
Multiscale Visualization and Scale-adaptive Modification of DNA Nanostructures
IEEE Transactions on Visualization and Computer Graphics, 24(1), January 2018. [
paper]
Lukas Lipp
Visualization of Fiber Orientation in Glass Fiber Reinforced Polymers
[
Bachelor Thesis]
Radu Jianu, Martin Krzywinski, Luana Micallef, Hsiang-Yun Wu
Mapifying the Genome, Scalable Set Visualizations (Dagstuhl Seminar 17332)
TR-193-02-2018-2, 2018 [
paper]
Stefan Dietrich
Smart Visibility Technique for Linear and Planar Molecular Assemblies
Tobias Klein, Ludovic Autin, Barbora Kozlikova, David Goodsell, Arthur Olson, Eduard Gröller, Ivan Viola
Instant Construction and Visualization of Crowded Biological Environments
IEEE Transactions on Visualization and Computer Graphics, 2018. [
paper]
Johannes Sorger
Integration Strategies in the Visualization of Multifaceted Spatial Data
Supervisor: Ivan Viola
Duration: 2013 — 2017
[
thesis]
Stefan Dietrich
SirTom - Structural information retaining Triangle-based Occlusion Management
[
Bachelor Thesis] [
image]
Stefan Stappen
Hybrid Frames - Animated Narrative Sequences in Molecular Visualization
[
teaser] [
thesis]
Guillermo Garcia-Escribano
Visual Evaluation of Computational Models of the Biological Mesoscale
Daniel Gehrer, Ivan Viola
Visualization of molecular machinery using agent-based animation
In Proceedings of SCCG 2017. May 2017.
[
paper]
David Kouřil, Mathieu Le Muzic, Barbora Kozlikova, Ivan Viola
Maya2cellVIEW: Integrated Tool for Creating Large and Complex Molecular Scenes
Poster shown at Spring Conference on Computer Graphics 2017
(May 2017)
Johannes Sorger, Peter Mindek, Peter Rautek, Eduard Gröller, Graham Johnson, Ivan Viola
Metamorphers: Storytelling Templates For Illustrative Animated Transitions in Molecular Visualization
In Proceedings of the Spring Conference on Computer Graphics 2017, pages 27-36. May 2017.
[
paper] [
teaser] [
video]
Daniel Gehrer
Visualization of molecular machinery using agent-based animation
[
image] [
Master thesis]
Peter Mindek, Johannes Sorger, David Kouřil, Tobias Klein, Graham Johnson, Ivan Viola
The Birth of a Virtual Cell
submitted to the Pacific Vis 2017 Storytelling Contest
Haichao Miao
Visualization and Modeling in DNA Nanotechnology,
April 2017, Inria, Grenoble, France
Lukas Mitterhofer
Modeling Microorganisms
[
Bachelor Thesis] [
image]
Ivan Kolesár, Stefan Bruckner, Ivan Viola, Helwig Hauser
A Fractional Cartesian Composition Model for Semi-Spatial ComparativeVisualization Design
IEEE Transactions on Visualization and Computer Graphics, 23(1), January 2017.
David Kouřil
Maya2CellVIEW: 3D Package Integrated Tool for Creating Large and Complex Molecular Scenes
Haichao Miao
Visualization of Brain Arteries, the Placenta and DNA Nanostructures in the Context of Abstraction,
2017, State Key Lab - Zhejiang University
Peter Mindek, David Kouřil, Johannes Sorger, David Toloudis, Blair Lyons, Graham Johnson, Eduard Gröller, Ivan Viola
Visualization Multi-Pipeline for Communicating Biology
IEEE Transactions on Visualization and Computer Graphics, 24(1), 2017. [
Paper] [
Preview Movie] [
Slides]
Viktor Vad, Jan Byska, Adam Jurcik, Ivan Viola, Eduard Gröller, Helwig Hauser, Sergio M. Margues, Jiri Damborsky, Barbora Kozlikova
Watergate: Visual Exploration of Water Trajectories in Protein Dynamics
In Eurographics Workshop on Visual Computing for Biology and Medicine 2017, pages 33-42. 2017.
Ludovic Autin, Peter Mindek
X-Mas Card 2016
[
Picture] [
X-Mas Card]
Barbora Kozlikova, Michael Krone, Martin Falk, Norbert Lindow, Daniel Baum, Ivan Viola, Marc Baaden, Julius Parulek, Hans-Christian Hege
Visualization of Biomolecular Structures: State of the Art Revisited
Computer Graphics Forum, (XX), November 2016.
Johannes Sorger, Peter Mindek, Tobias Klein, Graham Johnson, Ivan Viola
Illustrative Transitions in Molecular Visualization via Forward and Inverse Abstraction Transform
In Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM), pages 21-30. September 2016.
[
paper] [
video]
Peter Mindek
Multi-Scale Molecular Data Visualization,
3. May 2016, QCB Workshop on Visualizing & Modeling Cell Biology, Salt Lake City, Utah, USA
[Slides]
Jan Byska, Mathieu Le Muzic, Eduard Gröller, Ivan Viola, Barbora Kozlikova
AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics
IEEE Transactions on Visualization and Computer Graphics, 22(1):747-756, January 2016. [
Paper]
Viktor Vad, Douglas Cedrim, Wolfgang Busch, Peter Filzmoser, Ivan Viola
Generalized box-plot for root growth ensembles
BMC Bioinformatics, 2016.
Matthias Glinzner
Texturing of 3D Objects using Simple Physics and Equilateral Triangle Patches
[
paper]
Mathieu Le Muzic, Peter Mindek, Johannes Sorger, Ludovic Autin, David Goodsell, Ivan Viola
Visibility Equalizer: Cutaway Visualization of Mesoscopic Biological Models
Computer Graphics Forum, 35(3), 2016. [
Paper] [Slides]
Michael Krone, Barbora Kozlikova, Norbert Lindow, Marc Baaden, Daniel Baum, Julius Parulek, Hans-Christian Hege, Ivan Viola
Visual Analysis of Biomolecular Cavities: State of the Art
Computer Graphics Forum, 35(3):527-551, 2016. [
paper]
Matthias Reisacher, Mathieu Le Muzic, Ivan Viola
CellPathway: A Simulation Tool for Illustrative Visualization of Biochemical Networks
In Proceedings of WSCG. 2016.
[
paper]
Mathieu Le Muzic, Ludovic Autin, Julius Parulek, Ivan Viola
cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets
In Eurographics Workshop on Visual Computing for Biology and Medicine, pages 61-70. September 2015.
[
] [
paper]
Jan Byska, Adam Jurcik, Eduard Gröller, Ivan Viola, Barbora Kozlikova
MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids
Computer Graphics Forum, 3(34):1-10, May 2015. [
Paper]
Barbora Kozlikova, Michael Krone, Norbert Lindow, Martin Falk, Marc Baaden, Daniel Baum, Ivan Viola, Julius Parulek, Hans-Christian Hege
Visualization of Biomolecular Structures: State of the Art
In Eurographics Conference on Visualization (EuroVis) - STARs, pages 061-081. May 2015.
[
Paper]
Mathieu Le Muzic, Manuela Waldner, Julius Parulek, Ivan Viola
Illustrative Timelapse: A Technique for Illustrative Visualization of Particle Simulations on the Mesoscale Level
In Visualization Symposium (PacificVis), 2015 IEEE Pacific, pages 247-254. April 2015.
[
paper] [
screenshot]
Manuela Waldner, Mathieu Le Muzic, Matthias Bernhard, Werner Purgathofer, Ivan Viola
Attractive Flicker: Guiding Attention in Dynamic Narrative Visualizations
IEEE Transactions on Visualization and Computer Graphics, 20(12):2456-2465, December 2014. [
paper] [
Preview video] [
Submission video]
Ivan Kolesár, Julius Parulek, Ivan Viola, Stefan Bruckner, Anne-Kristin Stavrum, Helwig Hauser
Interactively illustrating polymerization using three-level model fusion
BMC Bioinformatics 2014, 15(345):1-16, October 2014.
Ivan Kolesár, Julius Parulek, Ivan Viola, Stefan Bruckner, Anne-Kristin Stavrum, Helwig Hauser
Illustrating Polymerization using Three-level Model Fusion
In Proceedings of IEEE BioVis 2014, pages 1-22. July 2014.
Mathieu Le Muzic, Julius Parulek, Anne-Kristin Stavrum, Ivan Viola
Illustrative Visualization of Molecular Reactions using Omniscient Intelligence and Passive Agents
Computer Graphics Forum, 33(3):141-150, June 2014. [
paper] [
video]
Julius Parulek, Daniel Jönsson, Timo Ropinski, Stefan Bruckner, Anders Ynnerman, Ivan Viola
Continuous Levels-of-Detail and Visual Abstraction for Seamless Molecular Visualization
Computer Graphics Forum, 33(6):276-287, May 2014.
Julius Parulek, Cagatay Turkay, Nathalie Reuter, Ivan Viola
Visual cavity analysis in molecular simulations
BMC Bioinformatics, 14(Suppl 19:S4 ):1-15, November 2013. [
Paper]
Johannes Sorger, Katja Bühler, Florian Schulze, Tianxiao Liu, Barry Dickson
neuroMAP - Interactive Graph-Visualization of the Fruit Fly's Neural Circuit
In Biological Data Visualization (BioVis), 2013 IEEE Symposium on , pages 73-80. October 2013.
Julius Parulek, Timo Ropinski, Ivan Viola
Seamless Visual Abstraction of Molecular Surfaces
In SCCG 2013 - 29th Proceedings Spring conference on Computer Graphics, pages 120-127. May 2013.
[
Paper]
Johannes Sorger
neuroMap - Interactive Graph-Visualization of the Fruit Fly’s Neural Circuit
[
Poster] [
Thesis]
Viktor Vad
Visualization in Root Phenotyping
Supervisor: Ivan Viola
Duration: March 2015 — 2017
Martina Rasch
Image-Space Solvent-Excluded Surface Visualization